miga-base 1.3.8.0 → 1.3.8.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 26e4d6df1a418582af445818b9965eaee00bb76282e5acd9fc1480d6b9d3e57b
-  data.tar.gz: 16c6f25a55191ca185fd4f5718e721780e718555525301ce98613290f7f38cc5
+  metadata.gz: 2e4abdd418e396b20fcfea4beaf4d70f3b0022808714478581e2e1f6f8a85478
+  data.tar.gz: 881884c4d5a933b64ac29e93397b62b7d1dc30fd599baaa8b6ac04a3ad3ab051
 SHA512:
-  metadata.gz: c38ef4522680e357f95c239de8529bd1c7f1be307243000e38dabfa592d99226ca5e228b56efa8918ad3ab55de75858f8fdec3ecaeef5d6471ec37af1a0d2fdc
-  data.tar.gz: 3ab0c91d807c27ceaeb412dffbdda2da29d8c558772988b5d8af6063ef9dee206329ff7caf9e5c5795b5ee5b0f019b8b8a0906eb3bb6daca4611b394b5b8df6d
+  metadata.gz: 317022ffe39818af13d36e3bf1e1adea80b3ab3aafb265b3df6371b6b5e87efdb75199cf8bd22aea37a63e941f824d1686f85bdb7a38eda3f4ba2a76c535b86b
+  data.tar.gz: 0d42dadd982374f0c618d76fc030f5665075e9973ca8e8615c5b090ab1dcc6bf663901a8f7355ce3bfa6874941d9098957d31704b6369474e516dd5ebf8c0b6b

data/lib/miga/cli/action/doctor.rb

@@ -50,8 +50,8 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
     # refdb:  ['ref-db', 'Check index format of reference databases'],
     status: ['status', 'Update metadata status of all datasets'],
     db:     ['databases', 'Check integrity of database files'],
-    bidir:  ['bidirectional', 'Check distances are bidirectional'],
     dist:   ['distances', 'Check distance summary tables'],
+    bidir:  ['bidirectional', 'Check distances are bidirectional'],
     files:  ['files', 'Check for outdated files'],
     cds:    ['cds', 'Check for gzipped genes and proteins'],
     ess:    ['essential-genes', 'Check for outdated essential genes'],

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 8, 0].freeze
+  VERSION = [1.3, 8, 2].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2023, 7, 5)
+  VERSION_DATE = Date.new(2023, 8, 8)
 
   ##
   # References of MiGA

data/utils/subclades.R

@@ -116,7 +116,8 @@ subclade_clustering <- function (out_base, thr, ani.d, dist_rds) {
     say("Subsampling large collection")
     ids <- sample(labels(ani.d), nMax)
     ani.d.ori <- ani.d
-    ani.d <- as.dist(as.matrix(ani.d)[ids, ids])
+    ani.d.m <- as.matrix(ani.d)
+    ani.d <- as.dist(ani.d.m[ids, ids])
   }
 
   # Silhouette
@@ -127,11 +128,12 @@ subclade_clustering <- function (out_base, thr, ani.d, dist_rds) {
   say("- Launch parallel jobs")
   s <- parSapply(
     cl, k,
-    function(x) {
+    function(x, ani.d) {
       library(cluster)
       s <- pam(ani.d, x, do.swap = FALSE, variant = "faster")$silinfo
       c(s$avg.width, -sum(ifelse(s$widths[, 3] > 0, 0, s$widths[, 3])))
-    }
+    },
+    ani.d = ani.d
   )
   say("- Stop cluster")
   stopCluster(cl)
@@ -156,9 +158,10 @@ subclade_clustering <- function (out_base, thr, ani.d, dist_rds) {
     ani.d <- ani.d.ori
     # Find closest medoid for missing genomes
     missing <- labels(ani.d)[!labels(ani.d) %in% names(ani.types)]
-    for (i in missing)
-      ani.types[i] <- which.min(as.matrix(ani.d)[ani.medoids, i])
+    say("- Classify:", length(missing))
+    for (i in missing) ani.types[i] <- which.min(ani.d.m[ani.medoids, i])
     # Reorder
+    say("- Reorder and save")
     ani.types <- ani.types[labels(ani.d)]
     # Save missing genomes for inspection
     write.table(
@@ -189,11 +192,16 @@ subclade_clustering <- function (out_base, thr, ani.d, dist_rds) {
   # Generate graphic report
   say("Graphic report")
   pdf(paste(out_base, ".pdf", sep = ""), 7, 12)
-  layout(matrix(c(rep(1:3, each = 2), 4:5), byrow = TRUE, ncol = 2))
-  plot_distances(ani.d)
-  plot_silhouette(k, s[1, ], s[2, ], ds, top.n)
-  if (!is.huge) plot_clustering(ani.cl, ani.d, ani.types)
-  if (!is.large) plot_tree(ani.ph, ani.types, ani.medoids)
+  if (is.huge) {
+    plot(NULL, axes = FALSE, xlab = '', ylab = '', xlim = 0:1, ylim = 0:1)
+    legend('center', legend = 'Dataset too large for graphical representation')
+  } else {
+    layout(matrix(c(rep(1:3, each = 2), 4:5), byrow = TRUE, ncol = 2))
+    plot_distances(ani.d)
+    plot_silhouette(k, s[1, ], s[2, ], ds, top.n)
+    plot_clustering(ani.cl, ani.d, ani.types)
+    if (!is.large) plot_tree(ani.ph, ani.types, ani.medoids)
+  }
   dev.off()
 
   # Save results

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.8.0
+  version: 1.3.8.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-07-05 00:00:00.000000000 Z
+date: 2023-08-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons